Analysis of combinatorial cis-regulation in synthetic and genomic promoters

项目摘要 当基因移动到新的染色体位置时，它们通常会以 不同层次我们将利用这些染色体位置效应来研究 染色体位置影响顺式调节序列（CRS）的活性。我们建议 衡量如何活动的一个大的和不同的收集CRS的变化时，他们是 转移到不同的染色体位置（目标1）。为了大规模收集这些数据，我们将引入 一种新的大规模平行报告基因检测（MPRA）。我们的目标是解决几个问题。 1.是什么原因导致了染色体之间调节潜力的差异 位置？当CRS的活动因移动到新位置而发生变化时， 由于新的染色质状态，附近增强子的活性，或两者的变化？ 2.什么时候CRS和基因组位置的调节作用是独立的，什么时候 它们以复杂的方式相互作用？相互作用是否取决于CRS和 特定的染色质景观？ 我们还建议补充我们的研究基因表达水平的研究 基因组位置如何影响基因表达动力学（目的2）。通过测量细胞- 在不同染色体位置由不同CRS产生的mRNA的细胞模式，我们将 揭示染色体环境如何改变表达的动力学。成功 完成这项建议的目标将导致定量和分子的理解 CRS和染色质环境对基因表达的组合调控。一个明确 了解CRS在基因组中的功能将有助于识别和解释疾病- 导致影响顺式调节的遗传变异。

Project Summary When genes move to new chromosomal locations they are often expressed at drastically different levels. We will use these chromosome position effects to investigate how different chromosomal locations affect the activity of cis-regulatory sequences (CRS). We propose to measure how the activities of a large and diverse collection of CRS change when they are moved to different chromosomal locations (Aim 1). To collect this data at scale we will introduce a new massively parallel reporter gene assay (MPRA). We aim to address several questions. 1. What accounts for the differences in regulatory potential between chromosome positions? When the activity of a CRS changes because it moves to a new location, are the changes due to the new chromatin state, the activity of nearby enhancers, or both? 2. When are the regulatory effects of CRS and genome position independent and when do they interact in complex ways? Do interactions depend on the properties of CRS and the specific chromatin landscape? We also propose to complement our investigation of gene expression levels with a study of how genome position influences gene expression dynamics (Aim 2). By measuring the cell- to-cell patterns of mRNA generated by different CRS at different chromosome locations, we will uncover how chromosome environments alter the dynamics of expression. The successful completion of the aims of this proposal will result in a quantitative and molecular understanding of the combinatorial regulation of gene expression by CRS and chromatin environment. A clear understanding of how CRS function in the genome will help identify and interpret disease- causing genetic variants that affect cis-regulation.